Dr Nicholas Clark
Dr

Nicholas Clark

Email: 
Phone: 
+61 7 535 15104

Background

An ecologist by training – I hold a B.Sc. (Hons) in Marine Ecology from the University of North Carolina, Wilmington and a Ph.D. in Ecological Modelling from Griffith University. I am broadly interested in exploring new ways to (1) understand how natural communities are formed and (2) predict how they will change over time. As an Amplify Fellow at UQ, my current research focuses on developing computational tools and adapting techniques from epidemiology and statistical forecasting to study how organisms and ecosystems respond to environmental change. This work is being applied to investigate natural dynamics for a range of natural systems including host-parasite interactions, wildlife populations and veterinary diseases.

I am an active member of the R community and have written and/or maintain several popular R packages. For example, I’m a lead developer on the MRFcov package for multivariate conditional random fields analyses. I also wrote the mvgam R package for fitting dynamic Generalised Additive Models to analyse and forecast multivariate ecological time series, and I regularly provide training seminars and workshops to help researchers learn techniques in ecological data analysis.

I am currently seeking Honours and PhD candidates with interests and/or skills in veterinary epidemiology, spatial / spatiotemporal modeling and quantitative ecology.

Availability

Dr Nicholas Clark is:
Available for supervision
Media expert

Fields of research

Biogeography and phylogeography Biological Sciences Biomedical and Clinical Sciences Community ecology (excl. invasive species ecology) Ecology Epidemiology Genetics Health Sciences Phylogeny and comparative analysis Population ecology Speciation and extinction

Qualifications

  • Doctor of Philosophy, Griffith University

Research interests

  • Using forecasts to anticipate how ecosystems respond to environmental change

    I am leading projects to develop new stastical and machine learning models that aim to advance our ability to predict and forecast ecological change. Expected applications of this work cover many fields where time series are very important, including conservation prioritisation, agriculture, species distribution modeling and biosecurity. Currently seeking both Honours and PhD students who are interested in ecological forecasting.

  • Automatic forecasting for non-Gaussian time series

    Automatic forecasting algorithms are crucial tools for many modern-day business operations. Yet nearly all of the available algorithms, and their associated software packages, assume that the series can be modelled with Gaussian errors. This makes it hard for end-users to employ these models when they routinely deal with non-Gaussian series, such as counts of sales, compositional data that must sum to 1, or time series that present as proportions. This project will develop extremely efficient and adaptable forecasting algorithms that can work with a huge variety of real-world time series, filling a crucial gap in the available software landscape for industry-level forecasting purposes.

  • The macroecology and biogeography of infectious dieases

    This work aims to describe large-scale patterns in the distributions of wildlife and their pathogens to identify processes governing ecological community assembly and the spread of pathogens. I'll be very happy to accept Honours or PhD students who are interested in biogeography, wildlife research and infectious disease epidemiology.

  • The epidemiology of animal pathogens across the human-wildlife interface

    I am interested in using molecular genetics and epidemiology to improve our understanding of how pathogen infection rates and emergence will change as human encroachment alters natural environments. This work mostly focuses on wildlife and domestic animals, but it can also be used to study human diseases. I'll be very happy to accept Honours or PhD students who are interested in this line of work.

Research impacts

My research is geared towards understanding how ecological communities, pathogen infection rates and pathogen emergence will change as climate change and human encroachment continue to alter natural environments. This work has generated translational benefits by helping to provide insights into factors that can be targeted to reduce the spread of pathogens in our animals and how to build better models for understanding wildlife responses to climate change. Some key media coverage of this body of work includes:

Ecological Forecasting with Dynamic Generalized Additive Models

Detecting how ecological communities respond to temperature changes

Understanding parasite spread through wildlife: the crucial role of statistical models

Adapting statistical network models to identify biotic interactions in changing communities

Using evolutionary models to trace the emergence of harmful viruses in pet dogs

Tracing the spread of fleas from pets to wildlife and vice versa

Detecting invasive malaria parasites in Australian birds

Search Professor Nicholas Clark’s works on UQ eSpace

72 works between 2012 and 2025
All (72) Journal Article (70) Conference Publication (2)

61 - 72 of 72 works

2017

Journal Article

A new look at the origins of gibbon ape leukemia virus

McKee, J., Clark, N., Shapter, F. and Simmons, G. (2017). A new look at the origins of gibbon ape leukemia virus. Virus Genes, 53 (2), 165-172. doi: 10.1007/s11262-017-1436-0

A new look at the origins of gibbon ape leukemia virus

2016

Journal Article

Co-infections and environmental conditions drive the distributions of blood parasites in wild birds

Clark, Nicholas J., Wells, Konstans, Dimitrov, Dimitar and Clegg, Sonya M. (2016). Co-infections and environmental conditions drive the distributions of blood parasites in wild birds. Journal of Animal Ecology, 85 (6), 1461-1470. doi: 10.1111/1365-2656.12578

Co-infections and environmental conditions drive the distributions of blood parasites in wild birds

2016

Journal Article

Why fly the extra mile? Using stress biomarkers to assess wintering habitat quality in migratory shorebirds

Aharon-Rotman, Yaara, Buchanan, Katherine L., Clark, Nicholas J., Klaassen, Marcel and Buttemer, William A. (2016). Why fly the extra mile? Using stress biomarkers to assess wintering habitat quality in migratory shorebirds. Oecologia, 182 (2), 385-395. doi: 10.1007/s00442-016-3679-1

Why fly the extra mile? Using stress biomarkers to assess wintering habitat quality in migratory shorebirds

2016

Journal Article

Molecular and morphological description of Haemoproteus (Parahaemoproteus) bukaka (species nova), a haemosporidian associated with the strictly Australo-Papuan host subfamily Cracticinae

Goulding, W., Adlard, R. D., Clegg, S. M. and Clark, N. J. (2016). Molecular and morphological description of Haemoproteus (Parahaemoproteus) bukaka (species nova), a haemosporidian associated with the strictly Australo-Papuan host subfamily Cracticinae. Parasitology Research, 115 (9), 3387-3400. doi: 10.1007/s00436-016-5099-x

Molecular and morphological description of Haemoproteus (Parahaemoproteus) bukaka (species nova), a haemosporidian associated with the strictly Australo-Papuan host subfamily Cracticinae

2016

Journal Article

Migration strategy and pathogen risk: non-breeding distribution drives malaria prevalence in migratory waders

Clark, Nicholas J., Clegg, Sonya M. and Klaassen, Marcel (2016). Migration strategy and pathogen risk: non-breeding distribution drives malaria prevalence in migratory waders. Oikos, 125 (9), 1358-1368. doi: 10.1111/oik.03220

Migration strategy and pathogen risk: non-breeding distribution drives malaria prevalence in migratory waders

2015

Journal Article

Specialist enemies, generalist weapons and the potential spread of exotic pathogens: malaria parasites in a highly invasive bird

Clark, Nicholas J., Olsson-Pons, Sophie, Ishtiaq, Farah and Clegg, Sonya M. (2015). Specialist enemies, generalist weapons and the potential spread of exotic pathogens: malaria parasites in a highly invasive bird. International Journal for Parasitology, 45 (14), 891-899. doi: 10.1016/j.ijpara.2015.08.008

Specialist enemies, generalist weapons and the potential spread of exotic pathogens: malaria parasites in a highly invasive bird

2015

Journal Article

Differences in host species relationships and biogeographic influences produce contrasting patterns of prevalence, community composition and genetic structure in two genera of avian malaria parasites in southern Melanesia

Olsson-Pons, Sophie, Clark, Nicholas J., Ishtiaq, Farah and Clegg, Sonya M. (2015). Differences in host species relationships and biogeographic influences produce contrasting patterns of prevalence, community composition and genetic structure in two genera of avian malaria parasites in southern Melanesia. Journal of Animal Ecology, 84 (4), 985-998. doi: 10.1111/1365-2656.12354

Differences in host species relationships and biogeographic influences produce contrasting patterns of prevalence, community composition and genetic structure in two genera of avian malaria parasites in southern Melanesia

2015

Journal Article

Molecular and morphological characterization of Haemoproteus (Parahaemoproteus) ptilotis, a parasite infecting Australian honeyeaters (Meliphagidae), with remarks on prevalence and potential cryptic speciation

Clark, Nicholas J., Adlard, Robert D. and Clegg, Sonya M. (2015). Molecular and morphological characterization of Haemoproteus (Parahaemoproteus) ptilotis, a parasite infecting Australian honeyeaters (Meliphagidae), with remarks on prevalence and potential cryptic speciation. Parasitology Research, 114 (5), 1921-1928. doi: 10.1007/s00436-015-4380-8

Molecular and morphological characterization of Haemoproteus (Parahaemoproteus) ptilotis, a parasite infecting Australian honeyeaters (Meliphagidae), with remarks on prevalence and potential cryptic speciation

2015

Journal Article

The influence of vagrant hosts and weather patterns on the colonization and persistence of blood parasites in an island bird

Clark, Nicholas J. and Clegg, Sonya M. (2015). The influence of vagrant hosts and weather patterns on the colonization and persistence of blood parasites in an island bird. Journal of Biogeography, 42 (4), 641-651. doi: 10.1111/jbi.12454

The influence of vagrant hosts and weather patterns on the colonization and persistence of blood parasites in an island bird

2014

Journal Article

First evidence of avian malaria in capricorn silvereyes (zosterops lateralis chlorocephalus) on heron island

Clark, Nicholas J., Adlard, Robert D. and Clegg, Sonya M. (2014). First evidence of avian malaria in capricorn silvereyes (zosterops lateralis chlorocephalus) on heron island. Sunbird, 44 (1), 1-11.

First evidence of avian malaria in capricorn silvereyes (zosterops lateralis chlorocephalus) on heron island

2014

Journal Article

A review of global diversity in avian haemosporidians (Plasmodium and Haemoproteus: Haemosporida): new insights from molecular data

Clark, Nicholas J., Clegg, Sonya M. and Lima, Marcos R. (2014). A review of global diversity in avian haemosporidians (Plasmodium and Haemoproteus: Haemosporida): new insights from molecular data. International Journal for Parasitology, 44 (5), 329-338. doi: 10.1016/j.ijpara.2014.01.004

A review of global diversity in avian haemosporidians (Plasmodium and Haemoproteus: Haemosporida): new insights from molecular data

2012

Journal Article

Ontogenetic shifts in the habitat associations of butterflyfishes (F. Chaetodontidae)

Clark, Nicholas J. and Russ, Garry R. (2012). Ontogenetic shifts in the habitat associations of butterflyfishes (F. Chaetodontidae). Environmental Biology of Fishes, 94 (4), 579-590. doi: 10.1007/s10641-011-9964-2

Ontogenetic shifts in the habitat associations of butterflyfishes (F. Chaetodontidae)

Past funding

  • 2022 - 2023
    Epidemiology of feline upper respiratory tract Infections in shelter cats at RSPCA Queensland
    Feline Health Research Fund
    Open grant
  • 2021 - 2024
    Towards reliable and explainable models for anticipating ecological change
    ARC Discovery Early Career Researcher Award
    Open grant
  • 2020 - 2023
    Deep sequencing of beta-tubulin genes to ascertain benzimidazole resistance mechanisms in canine hookworms in Australian dogs
    Research Donation Generic
    Open grant
  • 2019 - 2020
    TickAlert: development of an integrated early warning surveillance platform for tick paralysis
    UQ Early Career Researcher
    Open grant
  • 2017 - 2019
    Tracing the spillover of fleas and paralysis ticks between wildlife and domestic pets in Australia
    National Geographic Society
    Open grant

Availability

Dr Nicholas Clark is:
Available for supervision

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Supervision history

Current supervision

  • Doctor Philosophy

    Forecasting ecosystem responses to environmental change

    Principal Advisor

    Other advisors: Professor Ricardo Soares Magalhaes

  • Doctor Philosophy

    Evolutionary pathways and molecular characterization of Influenza Viruses at high-risk human-poultry interfaces in Bangladesh

    Associate Advisor

    Other advisors: Professor Ricardo Soares Magalhaes

  • Doctor Philosophy

    Dynamic habitat suitability modelling for terrestrial mammals in Australia integrating google earth engine, remote sensing, machine learning and citizen science data

    Associate Advisor

    Other advisors: Dr April Reside

  • Doctor Philosophy

    Volatile synchrony: Pulse reproductive events of giant canopy trees, and the fauna they impact.

    Associate Advisor

    Other advisors: Dr Andrew Letten

  • Doctor Philosophy

    Spatial epidemiological approaches to support local One Health strategies to achieve rabies infection control and elimination

    Associate Advisor

    Other advisors: Professor Ricardo Soares Magalhaes

  • Doctor Philosophy

    Prevalence of ticks and tick-borne diseases and other parasitic diseases in wild and free roaming canids in Queensland, Australia.

    Associate Advisor

    Other advisors: Dr Justine Gibson, Dr Swaid Abdullah

  • Doctor Philosophy

    Investigations into the importance of antimicrobial residues in the surveillance of antimicrobial resistance in peri-urban dairy farms of Nepal

    Associate Advisor

    Other advisors: Dr Deirdre Mikkelsen, Professor Peter Sly, Professor Ricardo Soares Magalhaes

Completed supervision

Enquiries

Contact Dr Nicholas Clark directly for media enquiries about:

  • Community ecology
  • Disease ecology
  • Ecological modeling
  • Forecasting
  • Host-parasite interactions

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